3RUL

New strategy to analyze structures of glycopeptide-target complexes

Structural Biology Knowledgebase: 3RUL SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.277
  • R-Value Work: 0.243

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3RUL

Classification: Signaling Protein / Antibiotic

Total Structure Weight: 43896.62

Macromolecule Entities
Molecule Chains Length Organism Details
Ubiquitin A, B, C, D 79 Homo sapiens Gene Name(s): UBC Gene View
Dalbavancin E, F, G, H 7 synthetic

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CL
Query on CL

B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
JSmol
M12
Query on M12

E, F, G, H 10-METHYLUNDECANOIC ACID
C12 H24 O2
QJRRBVNPIKYRQJ-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
MAN
Query on MAN

E, F, G, H ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer
 
JSmol
N1L
Query on N1L

E, F, G, H 2-AMINO-2-DEOXY-BETA-D-GLUCOPYRANURONIC ACID
C6 H11 N O6
CRIPFXSBMSGPKB-LVBGKUAWSA-N
Ligand Explorer
 
JSmol
TLA
Query on TLA

A, B L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
Ligand Explorer
 
JSmol
Modified Residues 8 Unique
ID Chains Type Formula 2D Diagram Parent
CCS
Query on CCS
A, B, C, D L-PEPTIDE LINKING C5 H9 N O4 S CYS
DAL
Query on DAL
A, B, C, D D-PEPTIDE LINKING C3 H7 N O2 --
HGM
Query on HGM
E, F, G, H D-peptide linking C9 H11 N O3 --
DTY
Query on DTY
E, F, G, H D-PEPTIDE LINKING C9 H11 N O3 --
HCL
Query on HCL
E, F, G, H L-peptide linking C8 H8 Cl N O4 --
GHP
Query on GHP
E, F, G, H D-PEPTIDE LINKING C8 H9 N O3 --
OMY
Query on OMY
E, F, G, H L-PEPTIDE LINKING C9 H10 Cl N O4 TYR
HG7
Query on HG7
E, F, G, H L-peptide linking C13 H21 N3 O2 --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.277
  • R-Value Work: 0.243
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 53.30 α = 90.00
b = 86.25 β = 90.00
c = 107.19 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-05-05
  • Released Date: 2012-06-06
  • Deposition author(s): Economou, N.J., Nahoum, V., Weeks, S.D., Grasty, K.C., Loll, P.J.

Revision History

No revisions since initial release